CIF Parser

https://xraytools.com/cifparse

Powder or single crystal

Reads a CIF and lays its crystallographic data out through a template, ready to paste into a manuscript or a thesis.

You supply: A CIF file, and a choice of HTML or LaTeX output.
Reading it: The result is shown both formatted and as source you can copy. The template is editable and can be re-submitted, so the table can be made to match a journal’s house style.

Next on the path: Interatomic Distances and Angles On How to read a published structure, step 1 of 4

Terms here: general position · multiplicity

Teaching with this page

Objective: After this page a learner can find the cell, the symmetry and the refinement table in a CIF and say what each item is.
Ask first: A CIF gives a cell edge as 5.6400(3) Å. What is the 3?
Watch for: “How many decimal places can be trusted”
Then: Interatomic Distances and Angles

Check yourself: A CIF gives a cell edge as 5.6400(3) Å. What is the 3?

The standard uncertainty, on the last digits quoted How many decimal places can be trusted

The bracketed figure is the standard uncertainty carried on the trailing digits, so this cell edge is 5.6400 ± 0.0003 Å. It is not a digit count and it is not a bound: it is one standard deviation from the refinement, which is why comparing two quantities means comparing their difference against both of theirs.

Input

CIF file

Maximum 5 MB. The file is stored under a hash of its contents.

Output format

HTML {$mytag} LaTeX 

Pick the one that matches the template below — it selects the delimiters the template is read with.

Template

<table class="cif">
 <tr>
 <td valign="top">cell</td>
 <td>
 a = {$CellLengthA} &#197; 
 b = {$CellLengthB} &#197; 
 c = {$CellLengthC} &#197; 
 V = {$CellVolume} &#197;3 
 </td>
 <td valign="top">
 &alpha; = {$CellAngleAlpha}° 
 &beta; = {$CellAngleBeta}° 
 &gamma; = {$CellAngleGamma}° 
 </td>
 </tr>
 <tr>
 <td></td>
 <td colspan="2">
 From {$CellMeasurementReflnsUsed} reflections between &theta;min = {$CellMeasurementThetaMin}{if $CellMeasurementThetaMin !== 'N/A'}°{/if} and &theta;max = {$CellMeasurementThetaMax}{if $CellMeasurementThetaMax !== 'N/A'}°{/if}.
 </td>
 </tr>
 <tr>
 <td>empirical formula sum</td>
 <td colspan="2">{$ChemicalFormulaSum}</td>
 </tr>
 <tr>
 <td>
 {if $Zprime !== NULL}
 Z', Z
 {else}
 Z
 {/if}
 </td>
 <td colspan="2">
 {if $Zprime !== NULL}
 {$Zprime}, {$CellFormulaUnitsZ}
 {else}
 {$CellFormulaUnitsZ}
 {/if}
 </td>
 </tr>
 <tr>
 <td>formula weight</td>
 <td colspan="2">{$ChemicalFormulaWeight} {if $ChemicalFormulaWeight !== 'N/A'}g mol&minus;1{/if}</td>
 </tr>
 <tr>
 <td>crystal system, space group</td>
 <td colspan="2">{$SpaceGroupCrystalSystem}, {$SpaceGroupNameHMAlt}</td>
 </tr>
 <tr>
 <td>crystal size</td>
 <td colspan="2">
 {if $ExptlCrystalSizeMax !== 'N/A' && $ExptlCrystalSizeMid !== 'N/A' && $ExptlCrystalSizeMin !== 'N/A'}
 ({$ExptlCrystalSizeMax} &times; {$ExptlCrystalSizeMid} &times; {$ExptlCrystalSizeMin}) mm3
 {else}
 N/A
 {/if}
 </td>
 </tr>
 <tr style="border-bottom: 1px solid black">
 <td>crystal colour, morphology</td>
 <td colspan="2">{$ExptlCrystalColour}, {$ExptlCrystalDescription}</td>
 </tr>
 <tr>
 <td>F(000)</td>
 <td colspan="2">{$ExptlCrystalF000}</td>
 </tr>
 <tr>
 <td>calculated density</td>
 <td colspan="2">{$ExptlCrystalDensityDiffrn} {if $ExptlCrystalDensityDiffrn !== 'N/A'}g cm&minus;3{/if}</td>
 </tr>
 <tr>
 <td>&theta;min, &theta;max</td>
 <td colspan="2">{$DiffrnReflnsThetaMin}, {$DiffrnReflnsThetaMax}</td>
 </tr>
 <tr>
 <td>completeness to &theta;full</td>
 <td colspan="2">{$DiffrnMeasuredFractionThetaFull} {if $DiffrnMeasuredFractionThetaFull !== 'N/A'}&percnt;{/if}</td>
 </tr>
 <tr>
 <td>wavelength</td>
 <td colspan="2">
 {if !empty($DiffrnRadiationTube)}{$DiffrnRadiationTube}{if $DiffrnRadiationTubeLine === 'Kalpha'}&nbsp;K&alpha;{/if},{/if}
 {$DiffrnRadiationWavelength} {if $DiffrnRadiationWavelength !== 'N/A'}&#197;{/if}
 </td>
 </tr>
 <tr>
 <td>measurement temperature</td>
 <td colspan="2">{$DiffrnAmbientTemperature} {if $DiffrnAmbientTemperature !== 'N/A'}K{/if}</td>
 </tr>
 <tr>
 <td>&mu;</td>
 <td colspan="2">{$ExptlAbsorptCoefficientMu} {if $ExptlAbsorptCoefficientMu !== 'N/A'}mm&minus;1{/if}</td>
 </tr>
 <tr>
 <td>diffractometer</td>
 <td colspan="2">{$DiffrnMeasurementDeviceType}</td>
 </tr>
 <tr>
 <td>Tmin, Tmax</td>
 <td colspan="2">{$ExptlAbsorptCorrectionTMin}, {$ExptlAbsorptCorrectionTMax}</td>
 </tr>
 <tr>
 <td>hkl range</td>
 <td colspan="2">
 {if $DiffrnReflnsLimitHMin !== 'N/A' && $DiffrnReflnsLimitHMax !== 'N/A' && $DiffrnReflnsLimitKMin !== 'N/A' && $DiffrnReflnsLimitKMax !== 'N/A' && $DiffrnReflnsLimitLMin !== 'N/A' && $DiffrnReflnsLimitLMax !== 'N/A'}
 h: {$DiffrnReflnsLimitHMin} &#8594; {$DiffrnReflnsLimitHMax}, k: {$DiffrnReflnsLimitKMin} &#8594; {$DiffrnReflnsLimitKMax}, l: {$DiffrnReflnsLimitLMin} &#8594; {$DiffrnReflnsLimitLMax}
 {else}
 N/A
 {/if}
 </td>
 </tr>
 <tr>
 <td>number of reflections</td>
 <td colspan="2">
 {if $DiffrnReflnsNumber !== 'N/A' && $ReflnsNumberTotal !== 'N/A' && $ReflnsNumberTotal !== 'N/A'}
 {$DiffrnReflnsNumber} [{$ReflnsNumberTotal} independent, {$ReflnsNumberGt} I > 2&sigma;(I)]
 {else}
 N/A
 {/if}
 </td>
 </tr>
 <tr>
 <td>Rint</td>
 <td colspan="2">{$DiffrnReflnsAvREquivalents}</td>
 </tr>
 <tr style="border-bottom: 1px solid black">
 <td>sin(&theta;) &lambda;&minus;1</td>
 <td colspan="2">{$SinThetaPerLambda} {if $SinThetaPerLambda !== 'N/A'}&#197;&minus;1{/if}</td>
 </tr>
 <tr>
 <td>R1 [I > 2&sigma;(I)]</td>
 <td colspan="2">{$RefineLsRFactorGt}</td>
 </tr>
 <tr>
 <td>wR2 (all reflections)</td>
 <td colspan="2">{$RefineLsWrFactorRef}</td>
 </tr>
 {if !empty($RefineLsAbsStructureFlack)}
 <tr>
 <td>Flack parameter</td>
 <td colspan="2">{$RefineLsAbsStructureFlack}</td>
 </tr>
 {/if}
 <tr>
 <td>S</td>
 <td colspan="2">{$RefineLsGoodnessOfFitRef}</td>
 </tr>
 <tr>
 <td>w</td>
 <td colspan="2">
 {if $RefineLsWeightingDetailsP2 !== 'N/A' && $RefineLsWeightingDetailsP !== 'N/A'}
 [&sigma;2(Fo2) + ({$RefineLsWeightingDetailsP2}P)2
 {if $RefineLsWeightingDetailsP !== 'N/A'}
 + {$RefineLsWeightingDetailsP}P
 {/if}
 ]&minus;1 with P = (Fo2 + 2Fc2)/3
 {else}
 N/A
 {/if}
 </td>
 </tr>
 <tr>
 <td>(&Delta;/&sigma;)max</td>
 <td colspan="2">{$RefineLsShiftPerSuMax}</td>
 </tr>
 <tr>
 <td>&Delta;&rho;max, &Delta;&rho;min</td>
 <td colspan="2">{$RefineDiffDensityMax} {if $RefineDiffDensityMax !== 'N/A'}e &#197;&minus;3{/if}, {$RefineDiffDensityMin} {if $RefineDiffDensityMin !== 'N/A'}e &#197;&minus;3{/if}</td>
 </tr>
 <tr>
 <td>number of data, parameters, restraints</td>
 <td colspan="2">{$RefineLsNumberReflns}, {$RefineLsNumberParameters}, {$RefineLsNumberRestraints}</td>
 </tr>
</table>

The following tags are supported: {$CellLengthA}, {$CellLengthB}, {$CellLengthC}, {$CellAngleAlpha}, {$CellAngleBeta}, {$CellAngleGamma}, {$CellVolume}, {$CellMeasurementReflnsUsed}, {$CellMeasurementThetaMin}, {$CellMeasurementThetaMax}, {$ChemicalFormulaSum}, {$Zprime}, {$CellFormulaUnitsZ}, {$ChemicalFormulaWeight}, {$SpaceGroupCrystalSystem}, {$SpaceGroupNameHMAlt}, {$ExptlCrystalSizeMax}, {$ExptlCrystalSizeMid}, {$ExptlCrystalSizeMin}, {$ExptlCrystalColour}, {$ExptlCrystalDescription}, {$ExptlCrystalF000}, {$ExptlCrystalDensityDiffrn}, {$DiffrnReflnsThetaMin}, {$DiffrnReflnsThetaMax}, {$DiffrnMeasuredFractionThetaFull}, {$DiffrnRadiationWavelength}, {$DiffrnRadiationTube}, {$DiffrnRadiationTubeLine}, {$DiffrnAmbientTemperature}, {$ExptlAbsorptCoefficientMu}, {$DiffrnMeasurementDeviceType}, {$ExptlAbsorptCorrectionTMin}, {$ExptlAbsorptCorrectionTMax}, {$DiffrnReflnsLimitHMin}, {$DiffrnReflnsLimitHMax}, {$DiffrnReflnsLimitKMin}, {$DiffrnReflnsLimitKMax}, {$DiffrnReflnsLimitLMin}, {$DiffrnReflnsLimitLMax}, {$DiffrnReflnsNumber}, {$ReflnsNumberTotal}, {$ReflnsNumberGt}, {$DiffrnReflnsAvREquivalents}, {$SinThetaPerLambda}, {$RefineLsRFactorGt}, {$RefineLsWrFactorRef}, {$RefineLsGoodnessOfFitRef}, {$RefineLsWeightingDetailsP}, {$RefineLsWeightingDetailsP2}, {$RefineLsShiftPerSuMax}, {$RefineDiffDensityMax}, {$RefineDiffDensityMin}, {$RefineLsNumberReflns}, {$RefineLsNumberParameters}, {$RefineLsNumberRestraints}, {$RefineLsAbsStructureFlack}.
HTML mode takes tags in the format of {$mytag}, LaTeX mode requires tags in the format of . This is necessary as curly braces are part of LaTeX standard syntax.
If _space_group_name_H-M_alt is not set within the CIF, it will automatically look for _symmetry_space_group_name_H-M. If _space_group_crystal_system is not found, it'll look for _symmetry_cell_setting.
Z' is calculated as Z' = Z / M where M is the multiplicity of a general position within the respective space group. The script looks for the space group number _space_group_IT_number.
This was tested on my CIFs. Surely, you will come up with many examples where things don't work or CIF items can't be identified. Feel free to send me your CIFs in order to make the script compatible. Also, let me know if you need more CIF items/tags.

Where this comes from

The crystallographic information file (CIF): a new standard archive file for crystallography
S. R. Hall, F. H. Allen and I. D. Brown, Acta Cryst. A 1991, 47, 655–685 · doi:10.1107/S010876739101067X
The format this page reads. The loop, the data name and the quoting rules a parser has to get right are all defined here — and the loop is the part a line-by-line reader gets wrong.